snATACseq analysis with ArchR - cluster QC 1.

Results

Cluster QC

No Harmony

Remove clusters that do not have >= 30 cells in at least 2 donors

  • Cell count before filter = 15235
  • Clusters to be retained from initial QC pass = C1, C11, C8, C6, C14, C3, C12, C13, C4, C5, C15, C7, C10, C9
  • No. of cells to be removed = 226
  • Cell count after filter = 15009

Reclustering plots

Batch corrected cell counts per cluster

C1 C10 C11 C12 C13 C14 C15 C16 C2 C3 C4 C5 C6 C7 C8 C9
1106 968 814 1036 417 1082 848 512 949 445 77 575 2643 559 638 2340

UMAPs

Unconstrained Integration

Cluster mappings

RNA ExN-4 RG-1 ExN-2 ExN-2 InN-1 RG-1 ExN-1 ExN-2 ExN-2 MG InN-2 InN-2 RG-2 ExN-2 ExN-5 ExN-2
ATAC C1 C15 C6 C9 C12 C5 C8 C10 C7 C4 C13 C14 C16 C11 C2 C3

Cell counts

UMAP

With Harmony

Remove clusters that do not have >= 30 cells in at least 2 donors

  • Cell count before filter = 15235
  • Clusters to be retained from initial QC pass = C1, C11, C8, C6, C14, C3, C12, C13, C4, C5, C15, C7, C10, C9
  • No. of cells to be removed = 226
  • Cell count after filter = 15009

Reclustering plots

UMAPs

Unconstrained Integration

Cluster mappings

RNA ExN-4 RG-1 ExN-2 ExN-1 InN-1 RG-2 ExN-1 ExN-5 RG-1 InN-2 ExN-5 InN-2 RG-1 ExN-2 ExN-4 InN-2 ExN-2
ATAC C3 C16 C9 C5 C12 C15 C8 C1 C6 C13 C2 C14 C17 C10 C4 C11 C7

Cell counts

UMAP